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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mergesketch.sh @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified December 19, 2019
7
8 Description: Merges multiple sketches into a single sketch.
9
10 Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
11
12 Usage: mergesketch.sh in=a.sketch,b.sketch out=c.sketch
13 With wildcards: mergesketch.sh *.sketch out=c.sketch
14
15 Standard parameters:
16 in=<file> Input sketches or fasta files; may be a comma-delimited
17 list. in= is optional so wildcards may be used.
18 out=<file> Output sketch.
19 amino=f Use amino acid mode.
20
21 Sketch-making parameters:
22 mode=single Possible modes, for fasta input:
23 single: Generate one sketch per file.
24 sequence: Generate one sketch per sequence.
25 autosize=t Produce an output sketch of whatever size the union
26 happens to be.
27 size= Restrict output sketch to this upper bound of size.
28 k=32,24 Kmer length, 1-32.
29 keyfraction=0.2 Only consider this upper fraction of keyspace.
30 minkeycount=1 Ignore kmers that occur fewer times than this. Values
31 over 1 can be used with raw reads to avoid error kmers.
32 depth=f Retain kmer counts if available.
33
34 Metadata parameters: (if blank the values of the first sketch will be used)
35 taxid=-1 Set the NCBI taxid.
36 imgid=-1 Set the IMG id.
37 spid=-1 Set the JGI sequencing project id.
38 name= Set the name (taxname).
39 name0= Set name0 (normally the first sequence header).
40 fname= Set fname (normally the file name).
41 meta_= Set an arbitrary metadata field.
42 For example, meta_Month=March.
43
44 Java Parameters:
45 -Xmx This will set Java's memory usage, overriding autodetection.
46 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
47 The max is typically 85% of physical memory.
48 -eoom This flag will cause the process to exit if an out-of-memory
49 exception occurs. Requires Java 8u92+.
50 -da Disable assertions.
51
52 For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
53 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
54 "
55 }
56
57 #This block allows symlinked shellscripts to correctly set classpath.
58 pushd . > /dev/null
59 DIR="${BASH_SOURCE[0]}"
60 while [ -h "$DIR" ]; do
61 cd "$(dirname "$DIR")"
62 DIR="$(readlink "$(basename "$DIR")")"
63 done
64 cd "$(dirname "$DIR")"
65 DIR="$(pwd)/"
66 popd > /dev/null
67
68 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
69 CP="$DIR""current/"
70
71 z="-Xmx4g"
72 z2="-Xms4g"
73 set=0
74
75 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
76 usage
77 exit
78 fi
79
80 calcXmx () {
81 source "$DIR""/calcmem.sh"
82 setEnvironment
83 parseXmx "$@"
84 if [[ $set == 1 ]]; then
85 return
86 fi
87 freeRam 3200m 84
88 z="-Xmx${RAM}m"
89 z2="-Xms${RAM}m"
90 }
91 calcXmx "$@"
92
93 sendsketch() {
94 local CMD="java $EA $EOOM $z -cp $CP sketch.MergeSketch $@"
95 # echo $CMD >&2
96 eval $CMD
97 }
98
99 sendsketch "$@"